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1 <tool name="GCA: Gene centered annotation" id="ceas_gca" version="0.1.0">
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2 <description>Find the nearest interval in the given intervals set fo every annotated coding gene</description>
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3 <macros>
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4 <import>ceas_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <command>
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8 gca -b $bfile --span=$span
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9 #include source=$gtpath_ceasdb_ref#
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10 --name=$name &> $log
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11 </command>
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12 <inputs>
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13 <param name="name" type="hidden" value="gca_out"/>
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14 <param ftype="bed" format="bed" name="bfile" type="data" label="BED file(100,000 lines max)">
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15 <validator type="unspecified_build" />
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16 </param>
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17 <expand macro="ceasdb_ref" />
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18 <param name="span" type="text" label="Span" value="3000">
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19 <validator type="in_range" max="1000000" min="100" message="Span is out of range, Span has to be between 100 to 1000000" />
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20 </param>
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21 </inputs>
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22 <outputs>
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23 <data format="xls" name="output" from_work_dir="gca_out.xls"/>
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24 <data format="txt" name="log" label="GCA job log"/>
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25 </outputs>
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26 <expand macro="stdio" />
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27 <tests>
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28 <test maxseconds="3600" name="GCA_1">
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29 <param name="bfile" value="peaks.bed" />
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30 <param name="span" value="3000" />
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31 <param name="refsrc" value="history"/>
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32 <param name="gdb" ftype="ceasdb" value="mm9.refGene.ceasdb"/>
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33 <output name="output">
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34 <assert_contents>
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35 <has_text_matching expression="NM_013495\tchr19\t3323300\t3385733\t+\t2994\t754\t31798\t224353\t0.07\t0.26\t0.12\t0.03\t0.0\t0.0\t0.0" />
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36 </assert_contents>
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37 </output>
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38 </test>
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39 </tests>
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40 <help>
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41 This tool finds the nearest binding sites in the given BED file for
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42 every annotated coding gene. It's a module in CEAS package which is
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43 written by Hyunjin Gene Shin, published in Bioinformatics (pubmed
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44 id:19689956).
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45
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46 @EXTERNAL_DOCUMENTATION@
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47
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48 @CITATION_SECTION@
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49
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50 .. class:: warningmark
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51
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52 **NEED IMPROVEMENT**
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53
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54 -----
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55
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56 **Parameters**
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57
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58 - **BED file** contains the transcription factor binding sites,
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59 generally the BED files for peaks from peak calling tools.
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60 - **Span** is the span for ChIP regions.
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61 - **Genome Annotation Version** to specify the annotations according to
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62 the data set. The annotations are downloaded from UCSC genome site.
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63
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64 -----
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65
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66 **Output**
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67
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68 - **XLS file** is the tab-delimited file.
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69
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70 -----
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71
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72 **script parameter list of GCA**
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73
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74 Options:
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75 --version show program's version number and exit
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76 -h, --help Show this help message and exit.
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77 -b BED, --bed=BED BED file of ChIP regions.
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78 -g GDB, --gt=GDB Gene annotation table. This can be a sqlite3 local db
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79 file, BED file or genome version of UCSC. The BED file
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80 must have an extension of '.bed'
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81 --span=SPAN Span in search of ChIP regions from TSS and TTS,
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82 DEFAULT=3000bp
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83 --name=NAME Experiment name. This will be used to name the output
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84 file. If an experiment name is not given, input BED
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85 file name will be used instead.
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86 --gn-group=GN_GROUP A particular group of genes of interest. If a txt file
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87 with one column of gene names (eg RefSeq IDs in case of
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88 using a refGene table) is given, gca returns the gene-
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89 centered annotation of this particular gene group.
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90 --gname2=NAME2 The gene names of --gn-group will be regarded as
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91 'name2.' See the schema of the gene annotation table.
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92
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93 </help>
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94
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95 </tool>
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